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Coexpression cluster:C3255

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Full id: C3255_pituitary_smallcell_maxillary_neuroblastoma_argyrophil_gastrointestinal_small



Phase1 CAGE Peaks

Hg19::chr12:131118370..131118390,-p5@ENST00000541840
Hg19::chr12:131118436..131118449,-p2@ENST00000541840
Hg19::chr12:131118454..131118470,-p1@ENST00000541840


Enriched pathways on this co-expression cluster<b>Summary:</b><br>Canonical pathway gene sets were compiled from Reactome, Wikipathways and KEGG. For the major signaling pathways, the transcriptionally-regulated genes (downstream targets) were obtained from Netpath. Combined, the canonical pathways and downstream targets totaled 489 human gene sets. The corresponding M. musculus gene sets were inferred by homology using the HomoloGene database. Enrichment for each of the canonical 489 pathways and gene sets included in the co-expression cluster was assessed by the hypergeometric probability. The resulting P values were also then adjusted by the Benjamini-Hochberg method for multiple comparisons.<br><b>Analyst: </b>Emmanuel Dimont<br><br>link to source dataset<br>data


No results for this coexpression

Enriched Gene Ontology terms on this co-expression cluster<b>Summary:</b> Results for GOStat analysis on co-expressed clusters. Each cluster with promoters mapping to at least two different genes was analysed with GOStat (PMID: 14962934) with default parameter. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br>data


No GOStat results

Enriched sample ontology terms on this co-expression cluster<b>Summary:</b>To summarize promoter activities (expression profile of a TSS region) across ~1000 samples, we performed enrichment analysis based on FANTOM5 Sample Ontology (FF ontology). The question here is “in which type of samples the promoter is more active”. To answer this question, we compared expressions (TPMs) in the samples associated with a sample ontology term and the rest of the samples by using the Mann-Whitney rank sum test. To summarize ontologies enriched in this co-expression cluster, we ran the same analysis on an averaged expression profile of all promoters that make up. <b>Analyst:</b> Hideya Kawaji <br><br>links to source dataset<br><br><br>uberon_data<br><br>


Uber Anatomy
Ontology termp-valuen
central nervous system5.60e-5582
neural tube1.29e-5457
neural rod1.29e-5457
future spinal cord1.29e-5457
neural keel1.29e-5457
regional part of nervous system1.43e-5494
nervous system1.43e-5494
regional part of forebrain1.47e-4641
forebrain1.47e-4641
future forebrain1.47e-4641
brain2.77e-4569
future brain2.77e-4569
anterior neural tube3.74e-4542
regional part of brain4.22e-4559
gray matter1.17e-4234
brain grey matter1.17e-4234
telencephalon2.60e-4234
regional part of telencephalon7.06e-4133
cerebral hemisphere5.68e-4032
neurectoderm1.54e-3890
neural plate3.52e-3886
presumptive neural plate3.52e-3886
adult organism5.57e-37115
cerebral cortex1.06e-3125
pallium1.06e-3125
pre-chordal neural plate2.47e-3061
regional part of cerebral cortex5.92e-2922
neocortex2.24e-2620
ectoderm2.83e-26173
presumptive ectoderm2.83e-26173
ectoderm-derived structure1.41e-25169
head8.55e-23123
anterior region of body9.46e-23129
craniocervical region9.46e-23129
tube1.42e-17194
temporal lobe2.97e-127
nucleus of brain3.11e-129
neural nucleus3.11e-129
basal ganglion5.79e-129
nuclear complex of neuraxis5.79e-129
aggregate regional part of brain5.79e-129
collection of basal ganglia5.79e-129
cerebral subcortex5.79e-129
organ part1.38e-11219
anatomical conduit4.18e-11241
posterior neural tube1.09e-1015
chordal neural plate1.09e-1015
gyrus1.26e-096
telencephalic nucleus2.23e-097
brainstem2.36e-098
epithelium3.24e-09309
embryo5.41e-09612
cell layer6.04e-09312
segmental subdivision of nervous system1.60e-0813
organ4.83e-08511
limbic system4.89e-085
anatomical cluster5.97e-08286
occipital lobe6.11e-085
gland of diencephalon8.54e-084
neuroendocrine gland8.54e-084
multi-tissue structure1.05e-07347
embryonic structure1.07e-07605
developing anatomical structure1.07e-07605
organism subdivision1.31e-07365
segmental subdivision of hindbrain2.31e-0712
hindbrain2.31e-0712
presumptive hindbrain2.31e-0712
germ layer2.73e-07604
embryonic tissue2.73e-07604
presumptive structure2.73e-07604
epiblast (generic)2.73e-07604


Overrepresented TFBS (DNA) motifs on this co-expression cluster<b>Summary:</b>The values shown are the p-values for overrepresentation of the motif in this coexpression cluster. So a small p-value means a strong overrepresentation. <b>Analyst:</b> Michiel de Hoon <br><br>link to source data <br> Novel motifs <br>data <br><br> Jaspar motifs <br>data


Novel motifs



JASPAR motifs

Motifs-log10(p-value)

{{{tfbs_overrepresentation_jaspar}}}



ENCODE TF ChIP-seq peak enrichment analysis<b>Summary:</b> For each TF and each co-expression cluster, the number of promoters with ENCODE TF ChIP signal was compared with the rest of promoters from the robust set using Fisher's exact test. Clusters with significant ChIP enrichment (q <= 0.05) after Benjamini-Hochberg correction were retained. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br><br>data


(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
NANOG#79923329.24477848101273.99627955670032e-050.000734801832081382



Relative expression of the co-expression cluster<b>Summary:</b>Co-expression clusters are compared against FANTOM5 samples to obtain relative expression. <br><b>Analyst:</b>NA<br><br>link to data source<br> data


This analysis result is provided for C0 - C305 clusters.